algoSD: Build algo object

In EU-ECDC/EpiSignalDetection: Signal Detection Analysis

Description

Build algo object from an sts object class using either FarringtonFlexible or GLRNB surveillance algorithm

Usage

algoSD(x.sts, algo = "FarringtonFlexible", timeUnit = "Month", testingPeriod = 5)

Arguments

x.sts	sts class object (see stsSD output)
algo	character string containing the name of the algorithm to use. Options are "FarringtonFlexible" (default) or "GLRNB".
timeUnit	character string for the time unit of the time series. Options are "Week" or "Month".
testingPeriod	numeric: number of time units (months, weeks) back in time to test the algorithm on (to detect outbreaks in)

Value

sts

See Also

stsSD plotSD

Examples

#-- Setting the parameters to run the report for
input <- list(
disease = "Salmonellosis",
country = "EU-EEA - complete series",
indicator = "Reported cases",
stratification = "Confirmed cases",
unit = "Month",
daterange = c("2010-01-01", "2016-12-31"),
algo = "FarringtonFlexible",
testingperiod = 5
)

#-- Example dataset
dataset <- EpiSignalDetection::SignalData

#-- Filtering on declared input parameters
dataset <- filterAtlasExport(dataset, input)

#-- Aggregating the data by geographical level and time point
dataset <- aggAtlasExport(dataset, input)

#-- Bulding the corresponding sts object
dataset.sts <- stsSD(observedCases = dataset$NumValue,
                     studyPeriod = dataset$StudyPeriod,
                     timeUnit = input$unit,
                     startYM = c(as.numeric(format(as.Date(input$daterange[1], "%Y-%m-%d"), "%Y")),
                                 as.numeric(format(as.Date(input$daterange[1], "%Y-%m-%d"), "%m"))))

#-- Building the corresponding algo object
dataset.algo <- algoSD(dataset.sts,
                       algo = input$algo,
                       timeUnit = input$unit,
                       testingPeriod =
                       input$testingperiod)

EU-ECDC/EpiSignalDetection documentation built on May 26, 2019, 2:36 a.m.